OK, my two boys wanted to make some aquatic characters: a gillman and a merfolk. Both are amphibious and can go on land or water. I'd like to write an adventure involving exploring a huge river like the Amazon, in a remote jungle. It would be big enough to have aquatic cities or ruins in the river and of course huge aquatic creatures. There could also be stuff going on above ground in the jungle. Any ideas for good plot hooks, types of locations, etc? Useful source books? Obviously I could make up my own locations, but is there a good regional setting for this on Golarion?

1) Escort or act as guards for someone or something moving up or down the river.
2) HEY! Who dammed the river? We're drying up here!
3) War or Peace - Journey to the gold rush boomtown to negotiate cessation of the polluting of the river from mining activity or engage in trade selling fish or other supplies to the boomtown or sabotage the mining (WAR!)
4) Take on some pirates or smugglers rescuing captives or otherwise disrupting their activities.
5) Find and explore the local equivalent of Atlantis.
6) Sahuagin http://paizo.com/pathfinderRPG/prd/monsters/sahuagin.html#_sahuagin
7) Local land dwellers need help dealing with some Skrags or Merrow (aquatic Trolls and Ogres respectively) that are charging tolls and harassing caravans crossing a local bridge. Fighting Scrags well underwater can be rather tricky (as in how do you use fire when your deep underwater or in an underwater cave <hehe>)
8) Variant of dammed river -> someone is altering the weather the river is either flooding or drying up badly.
9) Aboleth, another fun nasty aquatic creature. http://paizo.com/pathfinderRPG/prd/monsters/aboleth.html#_aboleth The pirates above are in turn dealing with Sahuagin who are in turn dealing with/enslaved by Aboleths.
10) A Hag coven is stirring up trouble. http://paizo.com/pathfinderRPG/prd/monsters/greenHag.html#_green-hag

As mentioned, Conrad's "Heart of Darkness" is sort of THE river adventure tale. The Humphrey Bogart film "The African Queen" is a great film version. "The Mosquito Coast", while not a river adventure per se, has elements of the genre. For a horror treatment, there's always "The Creature from the Black Lagoon"!

There's actually a Pathfinder scenario (for Pathfinder Society) which features a river-trek adventure: #3-09 "The Quest for Perfection, Part I: The Edge of Heaven", itself the first in an excellent trilogy of adventures.

Tropes of such an adventure (or mini-campaign) would include trouble with the boat (or maybe not, if they're swimming!), dangerous rapids and other hazards, being stalked by enigmatic, dangerous natives, and of course, monsters in the water.

They chill out during the day inside some underwater caves. At night, they've been dragging victims from a nearby village underwater either turning them, or eating them entirely. Recently, they've been attempting on capturing the village chief's young daughter.

Not helping matter, there's been a voodoo priestess (juju oracle) turning villagers from a different town nearby into living zombies. This voodoo woman is said to have a few witch cohorts and apprentices protecting her and coordinating attacks on the already rival village.

There is rumor that this voodoo woman and the vampires are working together. The town just wants to be left alone and the Chief wants his daughter safe. They employ this party to take care of the matter for a reward.

Cursed Waters

Long ago, there were many witch hunts in numerous villages along a large river. The villagers found burning witches a waste of fire wood and decided drowning witches was the best use of their available resources. The final witch they had caught, was the most powerful, many died to even subdue her. When being drowned she spoke a powerful curse, not upon the village, but upon the river.

It is said that those who delve into the water for more than an hour or two per day or drink too much from the water, then contracts a curse. The actual curse is unknown (DMs call, suggestions below) but what is known is that those who have swam in the water for too long or have drank too much of it, have vanished.

Aspiring witches, once followers of those witches drowned by the villages seek revenge on land for their masters and ancestors. While these witches are somewhat few and far between, they have hired skilled mercenaries and thieves for their causes and the party may come across them if they're unlucky.

Curse Suggestions: Turn into mermaids/mermen, slowly transformed into demons, allergic to sunlight, transported to a different underwater location to do battle (not a curse but meh), make them look like witches actions and all, etc...

Now, these are mostly just stories thought up, I don't DM much at all, just some ideas for exploration and easily altered if desired.

Just chiming in for the Guide to the River Kingdoms, reskinned for jungle. I direct your attention especially to the area called Outsea, a delightful little saltwater kingdom full of merfolk and sahuagin trapped deep inland. That would serve admirably as either a point of origin or a destination.

Such a river exploration sounds great fun.
I'd love to play in such a game.

Refering to the cursed waters idea:
I think turning the curse's victims into incorporeals could be a fun idea.

To Blood in the water:
In my opinion there are too many undead in the games already and I'd see it as a nice change to play a game of pathfinders without undead. But some players like them... so everyone their own.

I could even imagine your players stemming from Outsea, exploring the Sellen River all the way to the Inner Sea; to not getting into spoilers my idea becomes clear if you can read up on the origin of this settlement.

Seismic activity could be an interesting addition to a river campaign. Quakes can radically alter the course of rivers, create whirlpools out of nowhere or simply block them off with falling rock (itself an unexpected threat in the water).

How about dealing with the aftermath of a flood? If the affected townsfolk see your boys as river spirits/demons, they might beseech them for help or hold them accountable in any number of ways.

You might consider taking a look at Sean Russell's Swan's War trilogy. A pivotal element is a braided river with sections that can only be visited, or revisited with the help of magic. Flipped on its head that could mean your explorers take a left fork and suddenly find themselves in completely unfamiliar territory.

You also mentioned ruins in the water. I don't know if you feel like using anything resembling technology, but a functioning (or malfunctioning) old hydroelectric dam could be a very interesting dungeon setting within the river. There's an aberration made up of electric eels that would probably love it there.

In Robin Hobb's Liveship Traders books, there's a river characterized running through a seismically active region. Any time there's a quake, the waters run milky white and dissolve any organic material unfortunate enough to be in the water at the time (barring natively creatures adapted to the conditions). That might make a good environmental hazard to force the PCs out of the water at some point, or even a plot hook -- maybe a formerly pristine river has started going acid at intervals, and they need to find out why and stop it.

They chill out during the day inside some underwater caves. At night, they've been dragging victims from a nearby village underwater either turning them, or eating them entirely. Recently, they've been attempting on capturing the village chief's young daughter.

Not helping matter, there's been a voodoo priestess (juju oracle) turning villagers from a different town nearby into living zombies. This voodoo woman is said to have a few witch cohorts and apprentices protecting her and coordinating attacks on the already rival village.

There is rumor that this voodoo woman and the vampires are working together. The town just wants to be left alone and the Chief wants his daughter safe. They employ this party to take care of the matter for a reward.

Cursed Waters

Long ago, there were many witch hunts in numerous villages along a large river. The villagers found burning witches a waste of fire wood and decided drowning witches was the best use of their available resources. The final witch they had caught, was the most powerful, many died to even subdue her. When being drowned she spoke a powerful curse, not upon the village, but upon the river.

It is said that those who delve into the water for more than an hour or two per day or drink too much from the water, then contracts a curse. The actual curse is unknown (DMs call, suggestions below) but what is known is that those who have swam in the water for too long or have drank too much of it, have vanished.

Aspiring witches, once followers of those witches drowned by the villages seek revenge on land for their masters and ancestors. While these witches are somewhat few and far between, they have hired skilled mercenaries and thieves for their causes and the party may come across them if they're unlucky.

Curse Suggestions: Turn into mermaids/mermen, slowly transformed into demons, allergic to sunlight, transported to a different underwater location to do battle (not a curse but...

Re: Amphibious Vampires-

Alan Moore explored the concept to great effect early in his run on Swamp Thing. He elaborated a bit on how the Vampiric germ/virus/bacteria is anaerobic, can't stand oxygen, and so staking is harmful because it's opening vampires up and letting air inside them (which in turn comes from I Am Legend).

So the story was about a town put underwater by an artificial dam, and how the vampires had taken up residence and turned all flippery (oxygen in liquid form was perfectly fine, it seems), and a kind of queen vampire was allowed to evolve and even lay eggs, something that can't happen on dry land, according to the story.

Of particular interest to the river aspect might be the resolution:

spoiler!(for anyone planning on reading the story:

Swamp Thing uses his newfound elemental powers to rip apart the mountain that's damming the river, and so instead of being at the bottom of a still lake, the town is suddenly at the bottom of a rushing river. The running water destroys all the vampires, which are, after all, undead. Classic, actually.